ok i downloaded the new version of handbrake 0.9.5, it had ipad settings and apple tv2 and all that, my cell phone videos are converting good, now if i want to put movies on ipad using handbrake....ipad presets, MP4 File, or MKV File?

No, you can't.
As robertlc said, handbrake can't thransfer the movies to your iPad, it only convert the videos for your iPad, you should sync the converted video to iPad via iTunes library. Take this how to Sync Content to the iPad with iTunes to get the tips how to:
Sync video / movies to iPad with iTunes
Sync music to the iPad with iTunes
Sync pictures / photos to iPad with iTunes
Sync apps / applications to iPad with iTunes

Useful Searches

About iPadForums.net

iPadForums.net is a community dedicated to the Apple iPad. We discuss various topics including iPad Help, iPad Reviews, iPad Apps, iPad Accessories (such as iPad Keyboards, iPad Cases, iPad Covers), iPad Games and more.

iPadForums.net is not affiliated with Apple. We are an enthusiast site dedicated to everything Apple iPad (iPad 1 and iPad 2)